- phenixbb - phenix-online.org

Problems about AutoSol: too many HA sites identified.
by Kaibo Zhang 09 Jul '18

09 Jul '18

Hello, I tried to use AutoSol to solve a SAD date set. The space group is P212121, with two proteins per ASU each containing one SeMet. However, the Hyss would always find 4~5 extra sites per ASU besides the two SeMet residues. So my questions are: a. Is this normal to have so many more sites identified? Or what might be the problem? b. Could I remove those extra Se sites during refinement if the occupancy is low or doesn't make sense biologically? Here are some details: 1. Most of the extra sites are around 20% occupancy and not within the range as alternate SeMet side-chain positions. One of them even overlapped with the position where should be a ligand phosphate. 2. The 2Fo-Fc map and AutoBuild solution looked fine, but the Fo-Fc map is kinda noisy with positive peaks showing up within the main-chain density which causes troubles for refinement. 3. No twining was detected for the dataset. Several space groups have been tried (including no screw axis) and all of the solutions contained more sites than there should be. Please let me know if you encountered similar problems before. Thanks a lot! Best regards Kaibo *Kaibo Zhang* PULSe, Purdue University Hockmeyer Hall, Room 321 240 S. Martin Jischke Drive, West Lafayette, IN 47907 Telephone: 765-337-1955 E-mail: zhang644(a)purdue.edu

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Detrmining pixel size
by anaa2 08 Jul '18

08 Jul '18

Hello, Does anyone know how to accurately determine the voxel size of an EM map? If you are slightly off (i.e. 1.38 compared to 1.40 pixel) does this affect real space refinement in PHENIX? Many thanks, Noor

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Real space refinement
by Reza Khayat 08 Jul '18

08 Jul '18

Hi, What is the syntax for having phenix.real_space_refine refine a single chain of a multi-chain complex? I have separated the chains into distinct files and run refinement on a single chain (file) with undesirable results. It seems that residues adjacent to the density of a neighboring chain get pulled into the neighboring density -possibly because the neighboring density is vacant. I hope my explanation is clear. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070

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Fw: AsCA 2018/CRYSTAL 32 conference workshops
by Christopher Squire 06 Jul '18

06 Jul '18

? [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] Dear Colleagues, Registration for the AsCA 2018/CRYSTAL 32 Conference workshops which will be held on Sunday, 2 December 2018 is now open. Delegates can register for a workshop at the same time as registering for the conference. There are four workshops which will each run concurrently. Spaces are strictly limited, so please register now at the following site: http://asca2018.org/registration/? Workshop topics: * Olex2-CCDC workshop * CCP4-Autorickshaw workshop * Combined workshop 1) SBGrid - Structural biology software infrastructure, 2) Synergistic use of diffraction and spectroscopic methods at XFEL and synchrotron sources * LCP - Lipidic cubic phase workshop For a full description of the workshops visit http://asca2018.org/workshops/ and for the full programme (including times) visit http://asca2018.org/programme/. Finally, a reminder that submissions are now open. Please visit the Call for Abstracts<http://asca2018.org/call-for-abstracts/> page for more information and to submit an abstract. Should you have any queries regarding the AsCA 2018/CRYSTAL 32 Conference, please do not hesitate to contact us using the email address below. Kind regards, Event Services University of Auckland Email: asca2018(a)auckland.ac.nz<mailto:[email protected]> [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

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high level python API
by wtempel 06 Jul '18

06 Jul '18

Hi, I would like to call programs like phenix.refine from a python script. Is the python subprocess module my best bet? Or does phenix provide its own interface similar to, say, ccp4 dispatchers? Thanks. Wolfram Tempel

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Re: [phenixbb] [cctbxbb] Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 06 Jul '18

06 Jul '18

Hi Luc, No worries, let us know of any other concerns. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Fri, Jul 6, 2018 at 2:22 AM Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > Hi Billy, > > > Or do you need something sooner? > > No, considering the timeframe for the move to conda is before the end of > the year. I just wanted to know so that I can start advertising the change > to the people on my side. Sorry if I missed that point during the meeting > you invited me on. > > Best wishes, > > Luc > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

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Invitation to International conference "BIOMEMBRANES 2018"
by Marin, Egor 06 Jul '18

06 Jul '18

Fellow structural biologists, we are pleased to invite you to participate in the 4th biannual international C*onference* “BIOMEMBRANES 2018”, which will be held on October 1-5, 2018 at the Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia. This is the first meeting within the International Conference Series “Virtual Human – Imaging Across Scales” co-organized by scientists from Russia, Germany, China, and USA. Our speakers will focus on cutting-edge problems of modern integrative structural biology of biomembranes and membrane proteins, theoretical biophysics of membrane systems and computer modelling. The conference will highlight the role of biomembranes in aging and age-related diseases such as cancer, neurodegenerative (Alzheimer’s, Parkinson’s) and cardiovascular diseases. The talks will be given by world-leading scientists from Russia, USA, Germany, France, the Netherlands, China, Spain, Italy, Sweden and Switzerland. Preliminary scientific program, as well as the up-to-date list of speakers please find here: https://biomembranes2018.ru/program/ In parallel, an international *School* “Mechanisms of aging and age-related diseases” will take place as a satellite event of the Conference on September 30 - October 5, 2018. The full information about the school will soon be available on our web-site https://biomembranes2018.ru/sa tellite-events. Early bird registration until 31.07, registration until 14.09. Further information is available on the conference web site http://biomembranes2018.ru. We are looking forward to meet you in Dolgoprudny! sincerely yours, Organizing Committee

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Re: [phenixbb] [cctbxbb] Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 06 Jul '18

06 Jul '18

Hi Luc, With the planned migration to conda for dependencies, the idea is to build one linux installer using the compilers in conda (currently GCC 7.2, https://conda.io/docs/user-guide/tasks/build-packages/compiler-tools.html) and then test that installer on multiple distributions of linux. CentOS 7 would be one of the distributions used for testing. Or do you need something sooner? We currently do not build our installers on CentOS 7, but I have checked that the CentOS 6 installer runs and that the regression tests (phenix_regression.test_all_parallel, which is a superset of cctbx regression tests) pass on CentOS 7. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Wed, Jul 4, 2018 at 7:31 AM Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > Hi Billy, > > > The upcoming Phenix 1.14 official release will still have installers for > CentOS 5 and Windows 32-bit, but since CentOS is no longer supporting > CentOS 5, and RedHat is only supporting RHEL5 through their Extended Life > Cycle Support Add-On (until November 30, 2020), we are planning on > deprecating CentOS 5 support (32-bit and 64-bit). In addition, we are > planning on deprecating 32-bit support for Windows because only a few > percent (< 5% for both Windows and CentOS 5) of our Phenix downloads are > for 32-bit versions. > > > If you deprecate CentOS 5, will you start to support CentOS 7? I mean > right now, nightly tests run CentOS 5 & 6. Do you plan to make it 6 & 7? I > am asking so that I can start planning for Bruker among other things… > > Best wishes, > > Luc > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

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Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 02 Jul '18

02 Jul '18

Hi everyone, The upcoming Phenix 1.14 official release will still have installers for CentOS 5 and Windows 32-bit, but since CentOS is no longer supporting CentOS 5, and RedHat is only supporting RHEL5 through their Extended Life Cycle Support Add-On (until November 30, 2020), we are planning on deprecating CentOS 5 support (32-bit and 64-bit). In addition, we are planning on deprecating 32-bit support for Windows because only a few percent (< 5% for both Windows and CentOS 5) of our Phenix downloads are for 32-bit versions. Please let us know if support for CentOS 5 (32-bit and/or 64-bit) or 32-bit Windows is a requirement for your systems. If so, also please describe your setup. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Incorrect secondary structure assignment in a .pdb
by Maciej Jagielnicki 29 Jun '18

29 Jun '18

Hi All, I used a combination of phenix real space refine and Coot to build a model into a cryoEM density map. I used an existing .pdb file as a starting point for my building. During the build, some helical elements became strands and vice versa (it was very clear to my eyes). Unfortunately, neither Phenix nor Coot would automatically update the header information for secondary structure elements, and I had to manually edit the header so that helices would show up in correct places when the .pdb file was viewed in Chimera or similar software. Not an ideal way of doing this which is likely related to what happened next. When the header information is removed, however, as it happens when the pdb.extract tool prepares a .pdb file for submission by turning it into a .cif file, the secondary structure elements are still displayed when a .cif file is visualized (bizzare in itself) but also the secondary structure is taken straight from the starting .pdb file (the one I used as a base for my model to which there is no connection whatsoever). The question is this - where does the incorrect secondary information come from in the absence of the header? How to fix this? I cannot deposit a file that shows helices/sheets wherever it wants... Regards, Maciej J. -- Maciej Jagielnicki, MS. Graduate Student University of Virginia Molecular Physiology and Biological Physics 480 Ray C Hunt Drive Rm 320 Charlottesville, VA Lab Phone: 434-243-2520

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Call for targets (not-yet-released structures) for CASP13 modelling experiment
by Randy Read 28 Jun '18

28 Jun '18

Posted on behalf of the CASP organizing committee: **** NB: There are only two weeks left to collect new targets for CASP13, so your contributions would be very gratefully received! **** Request for protein structures to test modeling methods - CASP13 CASP community experiments aim to establish and advance the state of the art in protein structure modeling. To this end, CASP collects information on soon-to-be released experimental structures for a three month season every two years. Sequences and other information on these targets is distributed to the protein modeling community, and the resulting models assessed by independent experts in the field. Results are published in special issues of the journal PROTEINS (see all about CASP12 at https://onlinelibrary.wiley.com/toc/10970134/86/S1). About 100 modeling groups from around the world take part. The success of CASP depends completely on the generosity of the experimental community in providing modeling targets. We are now requesting targets for the CASP13 experiment, which will launch at the beginning of May. So, if you have anything suitable, we would be most grateful if you would go to the target entry page: http://www.predictioncenter.org/casp13/targets_submission.cgi The CASP community needs modeling targets over a wide range of difficulty, for modeling with and without the aid of templates. We are particularly interested in membrane proteins, protein complexes, and cryo-EM structures. We are also extending CASP to include more modeling assisted by sparse experimental data, in collaboration with experimental groups in NMR, SAXS, chemical crosslinking, and FRET. For that, protein material is needed (of course this is not expected for most targets, but if its available, it would be much appreciated!). For those of you who have not provided targets to CASP before, the procedure is simple – there is a web page for submitting targets, and an experienced staff to deal with any queries. We don’t need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. More details are available on the web site. Thanks, CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel, Switzerland ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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validating ~100 structures
by CPMAS Chen 26 Jun '18

26 Jun '18

Hi, All, I have about 100 structures needs be validated and optimized. what will be a fast way to do so? Can I somehow put phenix.molprobity in a circle? Thanks! -- *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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phenix.real_space_refine - Removing rotamer restraints on a per residue basis
by Ashley Pike 25 Jun '18

25 Jun '18

Hi, Is it possible to exclude particular residues from the effects of global restraints in phenix.real_space_refine? In my case rotamer restraints mucks up the sidechain fit to density for certain Phe and Tyr?. Thanks, Ashley

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Software Engineer position to work with Phaser team in Cambridge
by Randy Read 21 Jun '18

21 Jun '18

We've just advertised a position for a Software Engineer to work with us on the development of Phaser. Detailed information on the position and how to apply can be found on the University of Cambridge website (http://www.jobs.cam.ac.uk/job/17918/) and on jobs.ac.uk (http://www.jobs.ac.uk/job/BKS034/software-engineer). The text of the job description is appended, if you'd like to look at that before clicking on one of the links! Best wishes, Randy Read ================= We are looking for a graduate Software Engineer to join the group of Prof Read in the Cambridge Institute for Medical Research (http://www.cimr.cam.ac.uk/), based at the Cambridge Biomedical Campus in Cambridge. The well-established project develops mathematical methods and software for the imaging of biological molecules. The software supports academic and pharmaceutical R&D worldwide. You will be joining a small expert academic team. The successful applicant will have a careful approach to software development. Your software will be required to be reliable, algorithmically fast, and memory efficient. We have a slow development cycle and the code you write will be in use for the foreseeable future. Your individual contribution will be recognised with authorship of peer-reviewed articles; publications from our group have a track record of being highly cited. The project is funded by the National Institute of Health (USA) and the successful applicant will have the opportunity to join bi-annual collaborative meetings that cycle among Lawrence Berkeley National Laboratory (Berkeley, California), Duke University (Durham, North Carolina) and the New Mexico Consortium (Santa Fe, New Mexico). We also have an active collaboration with IBMB- CSIC (Barcelona, Spain). Software is open source (https://git.uis.cam.ac.uk/x/cimr-phaser/phaser.git/summary). We use the C++0x/C++11 standard to maintain cross-platform compilation and compatibility. You will have access to the University of Cambridge's computing resources, and a laptop will be provided. Qualifications and Experience: University degree that includes computer science and/or mathematics, experience with C++ and the Linux OS. Skills in Python scripting, GPU programming and threading would be desirable. Knowledge of biology to A level standard or equivalent would be an advantage. This appointment is full-time (37 hours/week Monday to Friday) but we welcome applications from individuals who wish to be considered for part-time working or other flexible working arrangements. Royalty payments from software will extend beyond the lifetime of the contract. University of Cambridge employment benefits include USS pension, and reduced staff fees for University of Cambridge graduate courses (see http://www.jobs.cam.ac.uk/offer/ for a full list). For more information on the research group see https://www.cimr.cam.ac.uk/research/principal-investigators/principal-inves…, and details of the Phaser project can be found at http://www.phaser.cimr.cam.ac.uk/. Fixed-term: The funds for this post are available untill 30th April 2022. ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Postdoctoral position in membrane protein structure and function at the NIH
by Anirban Banerjee 20 Jun '18

20 Jun '18

There is an open postdoctoral position for a membrane protein structure-function project in my lab at the NIH. We are currently focusing on integral membrane enzymes (Science. 2018, doi: 10.1126/science.aao6326) and transporters of transition metal ions (J Biol Chem. 2018, doi: 10.1074/jbc.M117.817478). Here is the formal announcement - EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT, BETHESDA, MD AND SURROUNDING AREA Position Description: The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We combine structural techniques such as macromolecular crystallography and cryo EM with biophysical and biochemical methods such as reconstitution based assays, high resolution light microscopy and small molecule screening to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. Our laboratory is part of the Cell Biology and Neurobiology Branch in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). We also have an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). Qualifications: The candidates should hold a Ph. D. degree, be author of at least one first author publication and have a strong background in biochemistry or structural biology. Experience with basic molecular biology, protein expression, purification and biochemical characterization are required. Prior experience in membrane protein biochemistry or mammalian expression system for protein purification will be added advantages. It is absolutely essential the candidate is motivated and prepared to put in the best efforts for fruition of the project goals. We are a small, friendly lab and ability to work as part of a cohesive group is important. To Apply: Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests. The NIH is dedicated to building a diverse community in its training and employment programs.

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Chair of the Department of Molecular Microbiology and Immunology at Univ. of Missouri
by Tanner, John J. 18 Jun '18

18 Jun '18

The Department of Molecular Microbiology and Immunology at the University of Missouri is searching for a new Chair. Please see the links below for information about the department and the position. I would be happy to discuss this opportunity offline with interested people. https://medicine.missouri.edu/departments/molecular-microbiology-immunology https://medicine.missouri.edu/sites/default/files/MMI_Chair_Advertisement-A… John J. Tanner Professor of Biochemistry and Chemistry Interim Chair of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-5635 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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Table 1 successor in 3D?
by Gerard Bricogne 13 Jun '18

13 Jun '18

Dear phenixbb subscribers, I sent the message below to the CCP4BB and phenixbb at the same time last Friday. It went straight through to the CCP4BB subscribers but was caught by the phenixbb Mailman because its size exceeded 40K. Nigel, as moderator of this list, did his best to rescue it, but all his attempts failed. He therefore asked me to resubmit it, now that he has increased the upper size limit. Apologies to those of you who are also CCP4BB subscribers, who will already have received this message and the follow-up discussion it has given rise to. With best wishes, Gerard. ----- Forwarded message from Gerard Bricogne <gb10> ----- Date: Fri, 1 Jun 2018 17:30:48 +0100 From: Gerard Bricogne <gb10> Subject: Table 1 successor in 3D? To: CCP4BB(a)JISCMAIL.AC.UK, phenixbb(a)phenix-online.org Dear all, Bernhard Rupp has just published a "Perspective" article in Structure, accessible in electronic form at https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2 in which part of his general argument revolves around an example (given as Figure 1) that he produced by means of the STARANISO server at http://staraniso.globalphasing.org/ . The complete results of his submission to the server have been saved and may be accessed at http://staraniso.globalphasing.org/Gallery/Perspective01.html and it is to these results that I would like to add some annotations and comments. To help with this, I invite the reader to connect to this URL, type "+" a couple of times to make the dots bigger, and press/toggle "h" whenever detailed information on the display, or selection of some elements, or the thresholds used for colour coding the displays, needs to be consulted. The main comment is that the WebGL interactive 3D display does give information that makes visible characteristics that could hardly be inferred from the very condensed information given in Table 1, and the annotations will be in the form of a walk through the main elements of this display. For instance the left-most graphical object (a static view of which is attached as "Redundancy.png") shows the 3D distribution of the redundancy (or multiplicity) of measurements. The view chosen for the attached picture shows a strong non-uniformity in this redundancy, with the region dominated by cyan/magenta/white having about twice the redundancy (in the 6/7/8 range) of that which prevails in the region dominated by green/yellow (in the 3/5 range). Clear concentric gashes in both regions, with decreased redundancy, show the effects of the inter-module gaps on the Pilatus 2M detector of the MASSIF-1 beamline. The blue spherical cap along the a* axis corresponds to HKLs for which no measurement is available: it is clearly created by the detector being too far from the crystal. The second (central) graphical object, of which a view is given in Figure 1 of Bernhard's article and another in the attached picture "Local_I_over_sigI.png") shows vividly the blue cap of measurements that were missed but would probably have been significant (had they been measured) cutting into the green region, where the local average of I/sig(I) ranges between 16 and 29! If the detector had been placed closer, significant data extending to perhaps 3.0A resolution would arguably have been measured from this sample. The right-most graphical object (of which a static view is attached as "Debye-Waller.png") depicts the distribution of the anisotropic Debye-Waller factor (an anisotropic generalisation of the Wilson B) of the dataset, giving yet another visual hint that good data were truncated by the edges of a detector placed too far. Apologies for such a long "STARANISO 101" tutorial but Bernhard's invitation to lift our eyes from the terse numbers in Table 1 towards 3D illustrations of data quality criteria was irresistible ;-) . His viewpoint also agrees with one of the main purposes of our STARANISO developments (beyond the analysis and remediation of anisotropy, about which one can - and probably will - argue endlessly) namely contribute to facilitating a more direct and vivid perception by users of the quality of their data (or lack of it) and to nurturing evidence-based motivation to make whatever extra effort it takes to improve that quality. In this case, the undeniable evidence of non-uniformity of redundancy and of a detector placed too far would give immediate practical guidance towards doing a better experiment, while statistics in Table 1 for the same dataset would probably not ... . Thank you Bernhard! With best wishes, Gerard, for and on behalf of the STARANISO developers ----- End forwarded message -----

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Coupling ligand occupancy with helix displacement
by John Michael Bruning 11 Jun '18

11 Jun '18

Hi, I have a very flexible covalent adduct that adopts three alternative conformations (A,B,C) in my structure . Conformations A and C are solvent exposed, while conformation B is buried. The buried conformation B displaces a regulatory helix (resseq 589:598) by a few angstrom, while the solvent exposed conformations do not displace this helix. I can't seem to write a occupancy .params file that fulfills: 1.) occ. of ligand conformation B = occ. of displaced helix conformation # coupling of ligand binding with helix displacement 2.) occ. non-displaced helix conformation = (1 - occ. displaced helix conformation) 3.) sum occ. ligand conformations A+B+C = 1 # assuming protein was initially labeled 100% It seems like #7 from http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12 is my situation, but I can't quite seem to modify this for my case. For example, something like: constrained_group { selection = chain A and resname CPE and altid B or chain A and resseq 589:598 and altid B} Captures the concerted conformation aspect (1) (occupancy for ligand conformation B = occupancy for displaced helix) and the sum occupancy of the displaced and non-displaced helix = 1 (2), but the sum of the the alternative conformations A+B+C > 1.0 (w/ A+C = 1.0) (3) Incidentally, my resolution is 2.4 Ang. Thanks for any help! Cheers, John Cheers, John *********************************** John Bruning, Post-Doctoral Scholar Stanford University, Glenn Lab CCSR Building, #3110 ***********************************

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CSHL X-ray Methods in Structural Biology Course Oct 15-30th 2018: Application deadline June 15th
by Paul Adams 05 Jun '18

05 Jun '18

Dear Colleagues, The June 15th deadline for applications to the CSHL X-ray Methods in Structural Biology Course to be held later this year, October 15 through October 30 2018, is rapidly approaching. This is a unique opportunity to become expert in the use of X-ray crystallography to solve challenging macromolecular structures. The official course announcement can be found here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=18 please pass this on to people who might be interested and who would benefit, including your students and postdocs. This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography, and consists of extensive lectures and practical sessions from experts in the field. The instructor team is: Alex McPherson, Bill Furey, Jim Pflugrath, Tassos Perrakis, and myself. We are assisted by world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation (see the course link above for more details). The goal of the course is for researchers who have had some exposure to X-ray crystallography to become experts. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. We expect participants to crystallize one or more proteins and determine their structures in a two week period. Students may also work on their own projects, but not exclusively. They will become very well-versed in the theory of X-ray diffraction and crystal structure determination, while also having lots of fun. Both synchrotron data collection and in-house diffraction data collection will be used to solve structures. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar and laboratory settings. Please check the above web link for more details. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. The course is supported with funds provided by the National Institute of General Medical Sciences, for which we are extremely grateful. Also there are stipends available from the Leona M. and Harry B. Helmsley Charitable Trust and the Howard Hughes Medical Institute to help offset the cost of tuition. If anyone has any questions, please send me an e-mail, we will be happy to answer all queries. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Fwd: phenixbb post from [email protected]
by Nigel Moriarty 04 Jun '18

04 Jun '18

Folks There was a post from Gerard Bricogne that was lost (as far as I can see) in the internals of MailMan because of a 40Kb size limit and other reasons unknown. It was posted to the CCP4BB so you may have already seen it. Please find it below. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov Subject: Table 1 successor in 3D? Dear all, Bernhard Rupp has just published a "Perspective" article in Structure, accessible in electronic form at https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2 in which part of his general argument revolves around an example (given as Figure 1) that he produced by means of the STARANISO server at http://staraniso.globalphasing.org/ . The complete results of his submission to the server have been saved and may be accessed at http://staraniso.globalphasing.org/Gallery/Perspective01.html and it is to these results that I would like to add some annotations and comments. To help with this, I invite the reader to connect to this URL, type "+" a couple of times to make the dots bigger, and press/toggle "h" whenever detailed information on the display, or selection of some elements, or the thresholds used for colour coding the displays, needs to be consulted. The main comment is that the WebGL interactive 3D display does give information that makes visible characteristics that could hardly be inferred from the very condensed information given in Table 1, and the annotations will be in the form of a walk through the main elements of this display. For instance the left-most graphical object (a static view of which is attached as "Redundancy.png") shows the 3D distribution of the redundancy (or multiplicity) of measurements. The view chosen for the attached picture shows a strong non-uniformity in this redundancy, with the region dominated by cyan/magenta/white having about twice the redundancy (in the 6/7/8 range) of that which prevails in the region dominated by green/yellow (in the 3/5 range). Clear concentric gashes in both regions, with decreased redundancy, show the effects of the inter-module gaps on the Pilatus 2M detector of the MASSIF-1 beamline. The blue spherical cap along the a* axis corresponds to HKLs for which no measurement is available: it is clearly created by the detector being too far from the crystal. The second (central) graphical object, of which a view is given in Figure 1 of Bernhard's article and another in the attached picture "Local_I_over_sigI.png") shows vividly the blue cap of measurements that were missed but would probably have been significant (had they been measured) cutting into the green region, where the local average of I/sig(I) ranges between 16 and 29! If the detector had been placed closer, significant data extending to perhaps 3.0A resolution would arguably have been measured from this sample. The right-most graphical object (of which a static view is attached as "Debye-Waller.png") depicts the distribution of the anisotropic Debye-Waller factor (an anisotropic generalisation of the Wilson B) of the dataset, giving yet another visual hint that good data were truncated by the edges of a detector placed too far. Apologies for such a long "STARANISO 101" tutorial but Bernhard's invitation to lift our eyes from the terse numbers in Table 1 towards 3D illustrations of data quality criteria was irresistible ;-) . His viewpoint also agrees with one of the main purposes of our STARANISO developments (beyond the analysis and remediation of anisotropy, about which one can - and probably will - argue endlessly) namely contribute to facilitating a more direct and vivid perception by users of the quality of their data (or lack of it) and to nurturing evidence-based motivation to make whatever extra effort it takes to improve that quality. In this case, the undeniable evidence of non-uniformity of redundancy and of a detector placed too far would give immediate practical guidance towards doing a better experiment, while statistics in Table 1 for the same dataset would probably not ... . Thank you Bernhard! With best wishes, Gerard, for and on behalf of the STARANISO developers

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d99 beyond Nyquist?
by Ricardo Righetto 03 Jun '18

03 Jun '18

Hi, I've seen the d99 criterion in phenix.mtriage reporting a resolution value beyond Nyquist (=2.0 A), or very close to Nyquist in another case. For these particular maps, which are from the same dataset processed with two different single-particle analysis packages (internal benchmarking), half-map FSC-based methods (including blocres) report resolutions in the range of 3.0-3.5 A which are consistent with the features I can see. How can I interpret this? I understand that d99 starts omitting Fourier samples from the corners of the reciprocal box, but does it make sense to report a value beyond Nyquist? I tried supplying unfiltered, masked and unmasked versions of the maps with barely any variation in the d99 results. Thanks in advance for helping figuring this out! Best wishes, -- Ricardo Diogo Righetto

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 01 Jun '18

01 Jun '18

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the July 2018 issue is 22 June 2018. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Table 1 successor in 3D?
by Gerard Bricogne 01 Jun '18

01 Jun '18

Dear all, Bernhard Rupp has just published a "Perspective" article in Structure, accessible in electronic form at https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2 in which part of his general argument revolves around an example (given as Figure 1) that he produced by means of the STARANISO server at http://staraniso.globalphasing.org/ . The complete results of his submission to the server have been saved and may be accessed at http://staraniso.globalphasing.org/Gallery/Perspective01.html and it is to these results that I would like to add some annotations and comments. To help with this, I invite the reader to connect to this URL, type "+" a couple of times to make the dots bigger, and press/toggle "h" whenever detailed information on the display, or selection of some elements, or the thresholds used for colour coding the displays, needs to be consulted. The main comment is that the WebGL interactive 3D display does give information that makes visible characteristics that could hardly be inferred from the very condensed information given in Table 1, and the annotations will be in the form of a walk through the main elements of this display. For instance the left-most graphical object (a static view of which is attached as "Redundancy.png") shows the 3D distribution of the redundancy (or multiplicity) of measurements. The view chosen for the attached picture shows a strong non-uniformity in this redundancy, with the region dominated by cyan/magenta/white having about twice the redundancy (in the 6/7/8 range) of that which prevails in the region dominated by green/yellow (in the 3/5 range). Clear concentric gashes in both regions, with decreased redundancy, show the effects of the inter-module gaps on the Pilatus 2M detector of the MASSIF-1 beamline. The blue spherical cap along the a* axis corresponds to HKLs for which no measurement is available: it is clearly created by the detector being too far from the crystal. The second (central) graphical object, of which a view is given in Figure 1 of Bernhard's article and another in the attached picture "Local_I_over_sigI.png") shows vividly the blue cap of measurements that were missed but would probably have been significant (had they been measured) cutting into the green region, where the local average of I/sig(I) ranges between 16 and 29! If the detector had been placed closer, significant data extending to perhaps 3.0A resolution would arguably have been measured from this sample. The right-most graphical object (of which a static view is attached as "Debye-Waller.png") depicts the distribution of the anisotropic Debye-Waller factor (an anisotropic generalisation of the Wilson B) of the dataset, giving yet another visual hint that good data were truncated by the edges of a detector placed too far. Apologies for such a long "STARANISO 101" tutorial but Bernhard's invitation to lift our eyes from the terse numbers in Table 1 towards 3D illustrations of data quality criteria was irresistible ;-) . His viewpoint also agrees with one of the main purposes of our STARANISO developments (beyond the analysis and remediation of anisotropy, about which one can - and probably will - argue endlessly) namely contribute to facilitating a more direct and vivid perception by users of the quality of their data (or lack of it) and to nurturing evidence-based motivation to make whatever extra effort it takes to improve that quality. In this case, the undeniable evidence of non-uniformity of redundancy and of a detector placed too far would give immediate practical guidance towards doing a better experiment, while statistics in Table 1 for the same dataset would probably not ... . Thank you Bernhard! With best wishes, Gerard, for and on behalf of the STARANISO developers

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Anisotropy with TLS
by Eugene Osipov 31 May '18

31 May '18

Hi, everyone, Can someone shed a light on B-factor refinement in PHENIX.refine. I am refining the structure with 2.5 A resolution, with individual B-factors and automatically defined TLS groups. Despite isotropic refinement of B-factors I still see ANISOU entries for atoms. I figured out that these ANISOU lines appear only after TLS refinement. So the question is how these ANISOU values are calculated? -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osipov(a)gmail.com

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Berkeley Server Downtown (5/29 - 5/31)
by Billy Poon 30 May '18

30 May '18

Dear all, On Tuesday, May 29, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available by 10:00 am Pacific on Thursday (5/31) at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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